Contacts of the helix formed by residues 210 - 217 (chain G) in PDB entry 2ONK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 210 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195G ASP* 3.4 24.8 + - - +
196G GLU* 5.0 5.2 - - + +
197G VAL* 4.7 0.9 - - - +
209G GLY* 1.3 78.7 - - - +
211G LEU* 1.3 69.4 + - - +
212G LYS* 4.7 4.3 - - + +
213G GLU* 3.0 34.8 + - + +
214G LEU* 2.9 21.2 + - - +
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Residues in contact with LEU 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239F LEU* 3.4 22.2 - - + -
30G LEU* 4.5 1.8 - - + -
190G ALA* 4.2 3.1 - - + +
191G ALA* 3.5 25.8 - - - +
197G VAL* 4.0 23.1 - - + +
209G GLY 4.4 0.2 + - - -
210G LYS* 1.3 71.4 - - - +
212G LYS* 1.3 68.2 + - + +
214G LEU* 2.7 26.0 + - + +
215G PHE* 3.0 29.6 + - + -
226G LEU* 4.1 18.2 - - + -
229G ARG* 3.3 32.5 - - - +
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Residues in contact with LYS 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237F LYS 6.1 0.2 - - - -
238F ILE 4.4 18.6 - - - +
239F LEU* 6.0 0.9 - - + -
240F ASP* 5.4 8.7 - - - +
210G LYS* 3.3 3.7 - - + +
211G LEU* 1.3 80.1 - - + +
213G GLU* 1.3 66.3 + - + +
215G PHE* 3.1 21.0 + - + +
216G SER* 3.4 13.9 + - - -
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Residues in contact with GLU 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209G GLY* 4.9 5.4 - - - -
210G LYS* 3.0 41.6 + - + +
212G LYS* 1.3 80.1 - - + +
214G LEU* 1.3 65.0 + - + +
216G SER* 3.1 20.5 + - - -
217G ALA* 3.2 16.5 + - + +
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Residues in contact with LEU 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G VAL* 3.7 42.6 - - + +
199G VAL* 4.1 11.7 - - + -
207G GLU* 4.1 32.8 - - + +
208G LYS 4.3 15.5 - - - +
209G GLY* 4.8 0.9 - - - -
210G LYS 2.9 19.2 + - - +
211G LEU* 2.7 23.1 + - + +
213G GLU* 1.3 74.3 - - + +
215G PHE* 1.3 61.1 + - - +
217G ALA* 3.7 12.8 - - - +
218G LYS* 4.8 1.6 - - - +
222G VAL* 4.6 14.3 - - + +
223G ALA* 5.2 3.1 - - - -
226G LEU* 3.4 19.8 - - + +
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Residues in contact with PHE 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239F LEU* 4.1 9.6 - - + -
240F ASP* 3.0 31.2 - - - +
211G LEU* 3.0 41.3 + - + -
212G LYS* 3.1 11.4 + - + +
214G LEU* 1.3 75.8 - - - +
216G SER* 1.3 70.4 + - - +
217G ALA 3.0 1.4 + - - -
218G LYS* 2.8 36.7 + - - +
223G ALA* 6.0 1.3 - - - +
226G LEU* 3.3 34.3 - - + -
229G ARG* 2.8 57.2 - - + -
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Residues in contact with SER 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G LYS 3.4 9.0 + - - -
213G GLU* 3.1 14.2 + - - -
215G PHE* 1.3 76.0 - - - +
217G ALA* 1.3 59.7 + - - +
218G LYS* 2.6 24.5 + - - +
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Residues in contact with ALA 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207G GLU* 4.6 5.5 - - - +
213G GLU* 3.2 15.3 + - + +
214G LEU* 3.7 9.8 - - - +
215G PHE 3.0 3.1 + - - -
216G SER* 1.3 75.8 + - - +
218G LYS* 1.3 58.1 + - - +
219G ASN* 3.0 28.3 + - - +
222G VAL* 6.0 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il